Job ID = 6457789 SRX = SRX4798826 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:55:34 prefetch.2.10.7: 1) Downloading 'SRR7965243'... 2020-06-21T11:55:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:57:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:57:40 prefetch.2.10.7: 'SRR7965243' is valid 2020-06-21T11:57:40 prefetch.2.10.7: 1) 'SRR7965243' was downloaded successfully Read 9127617 spots for SRR7965243/SRR7965243.sra Written 9127617 spots for SRR7965243/SRR7965243.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:19 9127617 reads; of these: 9127617 (100.00%) were unpaired; of these: 567376 (6.22%) aligned 0 times 7506229 (82.24%) aligned exactly 1 time 1054012 (11.55%) aligned >1 times 93.78% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 1471575 / 8560241 = 0.1719 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 21:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 21:03:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:03:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:03:13: 1000000 INFO @ Sun, 21 Jun 2020 21:03:21: 2000000 INFO @ Sun, 21 Jun 2020 21:03:28: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 21:03:34: 4000000 INFO @ Sun, 21 Jun 2020 21:03:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 21:03:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:03:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:03:41: 5000000 INFO @ Sun, 21 Jun 2020 21:03:43: 1000000 INFO @ Sun, 21 Jun 2020 21:03:49: 6000000 INFO @ Sun, 21 Jun 2020 21:03:50: 2000000 INFO @ Sun, 21 Jun 2020 21:03:56: 7000000 INFO @ Sun, 21 Jun 2020 21:03:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:03:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:03:56: #1 total tags in treatment: 7088666 INFO @ Sun, 21 Jun 2020 21:03:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:03:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:03:57: #1 tags after filtering in treatment: 7088497 INFO @ Sun, 21 Jun 2020 21:03:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:03:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:03:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:03:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:03:57: 3000000 INFO @ Sun, 21 Jun 2020 21:03:57: #2 number of paired peaks: 3412 INFO @ Sun, 21 Jun 2020 21:03:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:03:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:03:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:03:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:03:58: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 21:03:58: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 21:03:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.05_model.r INFO @ Sun, 21 Jun 2020 21:03:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:03:58: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Sun, 21 Jun 2020 21:04:04: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 21:04:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 21:04:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:04:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:04:11: 5000000 INFO @ Sun, 21 Jun 2020 21:04:13: 1000000 INFO @ Sun, 21 Jun 2020 21:04:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:04:19: 6000000 INFO @ Sun, 21 Jun 2020 21:04:20: 2000000 INFO @ Sun, 21 Jun 2020 21:04:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:04:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:04:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.05_summits.bed INFO @ Sun, 21 Jun 2020 21:04:25: Done! pass1 - making usageList (300 chroms): 2 millis pass2 - checking and writing primary data (6219 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:04:26: 7000000 INFO @ Sun, 21 Jun 2020 21:04:27: 3000000 INFO @ Sun, 21 Jun 2020 21:04:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:04:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:04:27: #1 total tags in treatment: 7088666 INFO @ Sun, 21 Jun 2020 21:04:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:04:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:04:27: #1 tags after filtering in treatment: 7088497 INFO @ Sun, 21 Jun 2020 21:04:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:04:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:04:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:04:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:04:28: #2 number of paired peaks: 3412 INFO @ Sun, 21 Jun 2020 21:04:28: start model_add_line... INFO @ Sun, 21 Jun 2020 21:04:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:04:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:04:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:04:28: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 21:04:28: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 21:04:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.10_model.r INFO @ Sun, 21 Jun 2020 21:04:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:04:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:04:33: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:04:39: 5000000 INFO @ Sun, 21 Jun 2020 21:04:46: 6000000 INFO @ Sun, 21 Jun 2020 21:04:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:04:52: 7000000 INFO @ Sun, 21 Jun 2020 21:04:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:04:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:04:52: #1 total tags in treatment: 7088666 INFO @ Sun, 21 Jun 2020 21:04:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:04:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:04:52: #1 tags after filtering in treatment: 7088497 INFO @ Sun, 21 Jun 2020 21:04:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:04:52: #1 finished! INFO @ Sun, 21 Jun 2020 21:04:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:04:52: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:04:53: #2 number of paired peaks: 3412 INFO @ Sun, 21 Jun 2020 21:04:53: start model_add_line... INFO @ Sun, 21 Jun 2020 21:04:53: start X-correlation... INFO @ Sun, 21 Jun 2020 21:04:53: end of X-cor INFO @ Sun, 21 Jun 2020 21:04:53: #2 finished! INFO @ Sun, 21 Jun 2020 21:04:53: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 21:04:53: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 21:04:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.20_model.r INFO @ Sun, 21 Jun 2020 21:04:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:04:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:04:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:04:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:04:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.10_summits.bed INFO @ Sun, 21 Jun 2020 21:04:55: Done! pass1 - making usageList (216 chroms): 1 millis pass2 - checking and writing primary data (2324 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:05:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:05:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:05:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:05:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798826/SRX4798826.20_summits.bed INFO @ Sun, 21 Jun 2020 21:05:22: Done! pass1 - making usageList (93 chroms): 1 millis pass2 - checking and writing primary data (584 records, 4 fields): 6 millis CompletedMACS2peakCalling